NM_001377299.1(NDUFS2):c.629T>C (p.Met210Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 22, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003068807.3

Allele description [Variation Report for NM_001377299.1(NDUFS2):c.629T>C (p.Met210Thr)]

NM_001377299.1(NDUFS2):c.629T>C (p.Met210Thr)

Gene:

NDUFS2:NADH:ubiquinone oxidoreductase core subunit S2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_001377299.1(NDUFS2):c.629T>C (p.Met210Thr)

HGVS:

NC_000001.11:g.161209858T>C
NG_013352.1:g.15544T>C
NM_001166159.2:c.629T>C
NM_001377298.1:c.629T>C
NM_001377299.1:c.629T>CMANE SELECT
NM_001377300.1:c.629T>C
NM_001377301.1:c.629T>C
NM_001377302.1:c.629T>C
NM_001410889.1:c.629T>C
NM_004550.5:c.629T>C
NP_001159631.1:p.Met210Thr
NP_001364227.1:p.Met210Thr
NP_001364228.1:p.Met210Thr
NP_001364229.1:p.Met210Thr
NP_001364230.1:p.Met210Thr
NP_001364231.1:p.Met210Thr
NP_001397818.1:p.Met210Thr
NP_004541.1:p.Met210Thr
NC_000001.10:g.161179648T>C
NR_165188.1:n.648T>C

Protein change:

M210T

Molecular consequence:

NM_001166159.2:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377298.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377299.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377300.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377301.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377302.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001410889.1:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004550.5:c.629T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_165188.1:n.648T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Microbe sample from Enterococcus faecalis
Microbe sample from Enterococcus faecalis

biosample
Selliguea hellwigii voucher Hovenkamp s.n. (L) trnL-trnF intergenic spacer, part...
Selliguea hellwigii voucher Hovenkamp s.n. (L) trnL-trnF intergenic spacer, partial sequence; chloroplast
gi|160693478|gb|EU128518.1|

Nucleotide
PREDICTED: Accipiter gentilis SHC adaptor protein 3 (SHC3), transcript variant X...
PREDICTED: Accipiter gentilis SHC adaptor protein 3 (SHC3), transcript variant X1, mRNA
gi|2280412575|ref|XM_049796654.1|

Nucleotide
Enterococcus faecalis strain KS3H-124 chromosome, complete genome
Enterococcus faecalis strain KS3H-124 chromosome, complete genome
gi|2663062063|gb|CP142808.1|

Nucleotide
rab GTPase-activating protein 1 isoform X1 [Homo sapiens]
rab GTPase-activating protein 1 isoform X1 [Homo sapiens]
gi|767956806|ref|XP_011516743.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003456460	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003456460

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 22, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003456460.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 210 of the NDUFS2 protein (p.Met210Thr). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with NDUFS2-related conditions. This variant is present in population databases (rs751068903, gnomAD 0.03%).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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